Abstract
Actinidia chinensis is an important economic plant belonging to the basal lineage of the asterids. Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement. We report here the complete nucleotide sequences of the chloroplast genomes for Actinidia chinensis and A. chinensis var deliciosa obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The total genome size ranges from 155,446 to 157,557 bp, with an inverted repeat (IR) of 24,013 to 24,391 bp, a large single copy region (LSC) of 87,984 to 88,337 bp and a small single copy region (SSC) of 20,332 to 20,336 bp. The genome encodes 113 different genes, including 79 unique protein-coding genes, 30 tRNA genes and 4 ribosomal RNA genes, with 16 duplicated in the inverted repeats, and a tRNA gene (trnfM-CAU) duplicated once in the LSC region. Comparisons of IR boundaries among four asterid species showed that IR/LSC borders were extended into the 5’ portion of the psbA gene and IR contraction occurred in Actinidia. The clap gene has been lost from the chloroplast genome in Actinidia, and may have been transferred to the nucleus during chloroplast evolution. Twenty-seven polymorphic simple sequence repeat (SSR) loci were identified in the Actinidia chloroplast genome. Maximum parsimony analyses of a 72-gene, 16 taxa angiosperm dataset strongly support the placement of Actinidiaceae in Ericales within the basal asterids.
Highlights
In plants, chloroplasts are key organelles for photosynthesis and are crucial in the biosynthesis of starch, fatty acids, pigments and amino acids [1]
Four junction regions between inverted repeat (IR) and small-single-copy region (SSC)/large-single-copy region (LSC) in each cp genome were confirmed by PCR amplifications and Sanger sequencing
The complete chloroplast sequence of Actinidia of the basal asterid was obtained with Illumina sequencing technology and Sanger sequencing
Summary
Chloroplasts (cp) are key organelles for photosynthesis and are crucial in the biosynthesis of starch, fatty acids, pigments and amino acids [1]. The Complete Chloroplast Genome Sequence of Kiwifruit genomes, chloroplast genomes are largely conserved in gene content, organization and structure [3]. Complete plastid genome sequences of vascular plants were first reported in tobacco [5]. Over 600 cp genome sequences are currently deposited at the National Center for Biotechnology Information (NCBI) including all of the major lineages of the plant kingdom. Only three complete cp genomes have been sequenced for representatives of the basal asterids: Ardisia polysticta (Myrsinaceae) [6], Camellia sinensis (Theaceae) [7], and Vaccinium macrocarpon (Ericaceae) [8]. More cp genome sequences from additional taxa of the basal asterids are needed for understanding phylogenetic relationships among angiosperms [7]
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